Habitat micromodification poses significant challenges to wildlife, necessitating adaptive responses. This study aimed to investigate how such habitat alterations affect the dietary intake and gut microbiota of Père David’s deer (Elaphurus davidianus). A total of 25 fresh fecal samples were collected from Père David’s deer through non-invasive sampling in Tianjin Qilihai Wetland across three distinct phases of habitat micromodification: pre-change (N = 10), under-change (N = 8), and post-change (N = 7). Dietary composition was analyzed via microscopic identification of plant residues, and gut microbiota structure was characterized using 16S rRNA high-throughput sequencing. Results showed that the diet shifted significantly across phases, with 33 plant species from 20 families identified. Meanwhile, the core gut microbiota remained structurally stable. The phyla Firmicutes and Bacteroidota consistently dominated, despite fluctuations in some specific bacterial genera. Functional prediction indicated minimal change in core microbial metabolic pathways. Correlation analysis suggested that key dietary plants were linked to the abundance of specific, functionally relevant microbial taxa. In conclusion, this study demonstrates that the gut microbiota of Père David’s deer exhibits marked resilience to dietary shifts induced by habitat micromodification. This stability is underpinned by functional redundancy within the microbial community and the consistent intake of fibrous plants, representing a key adaptive mechanism. Our findings highlight that integrating non-invasive monitoring of diet and microbiota can effectively assess the adaptive capacity of endangered ungulates to managed habitat change, thereby informing more resilient conservation strategies.